Chemical cognitive ability is a fundamental aspect of effective chemistry education, facilitating students’ understanding of essential concepts such as substance structure, chemical transformations, and atomic bonding processes. Augmented reality (AR) technology has emerged as a promising tool in science education, offering immersive learning experiences that enhance students’ comprehension of chemical phenomena. This study explored the utilization of AR applications, specifically QuimiAR, in the designing of six simulation videos focusing on chemical bonding processes. These videos were integrated into a teaching method centered around the topic “Chemical Bonding” and implemented in a secondary school classroom in Hanoi, Vietnam, comprising 32 students. Following the AR-enhanced teaching session, students’ chemistry cognitive ability was evaluated using three methods: standardized tests assessing five criteria of chemistry cognitive ability according to the Vietnamese educational curriculum; surveys gauging students’ interest and knowledge acquisition using AR; and in?depth interviews. The results indicate that AR usage significantly increased students’ engagement in learning, enhanced their understanding of substance composition and chemical bonding processes, and improved their ability to apply knowledge to solve learning challenges. This research provides practical guidance for educators in leveraging the advantages of QuimiAR software to design simulations focusing on chemical bonding, thereby fostering students’ cognitive ability in chemistry. By expanding the use of AR technology to create various chemical simulations, teachers can cultivate students’ cognitive abilities in chemistry, promoting active learning and facilitating academic success.